Is the enclosure that you're talking about indoors or out? If it's outdoors, could you tell us what country you live in (in the UK it is far too cold to have a tortoise in an enclosure outdoors now), and if it's indoors then I think that if there are mushrooms growing out of the substrate then it's too wet for a Mediterranean tortoise like a Hermann's. What sort of lighting and heating arrangements do you have in the enclosure, and what temperature is it at the hot end and the cool end (you want around 30C directly under the heat source, and the temperature should be measured at the height of the tortoise's shell, and not by a thermometer on a nearby wall), and about 20C at the cool end. I think that with those temperatures it would be unlikely that mushrooms would grow and so it might just be too cool and damp. Could you possibly send us a photo of enclosure?
I would definitely remove the mushrooms, as they could well be poisonous ones, and I would also remove the slugs as sometimes tortoises eat them and this isn't good for them. The best way to remove waste is just to spot clean it every day or two.
You probably already have one, but in case you don't, here's a link to a care sheet for Hermann's https://www.tortoise-protection-group.o ... 014New.pdf .
I'm sure we can get the mushroom problem resolved, and a photo would help a lot. A photo of your tortoise in his enclosure would be even better, as we never get tired of looking at photos of lovely tortoises!
Nina